Rodrigo Duterte said he hurled a Chinese man suspected of rape and murder out mid-air.
He said: “If you are corrupt, I will fetch you using a helicopter to Manila and I will throw you out. I have done this before, why would I not do it again?”
Mr Duterte’s spokesman described the alleged incident as an “urban legend”.
The latest controversy comes just weeks after Mr Duterte admitted killing people during the 22 years he spent as mayor of Davao City, in the south of the country.
He claimed to have toured the city’s streets on his motorcycle looking for drug dealers to shoot.
His comments sparked international condemnation and created tensions with the United States and United Nations.
Since his election in May, more than 6,100 people have been killed in Mr Duterte’s war on drugs.
About a third of the victims have been killed by police but vigilantes are also responsible for many of the deaths.
Despite criticism of the killings, the Philippines president has pledged to continue his crackdown.
He said: “Until the last pusher is out of the street … until the last drugs lord is killed, this drug campaign would continue to the last day of my term.”
On Wednesday night two unknown gunmen on motorbikes shot dead seven people in a drugs den in the capital Manila.
Four of those killed were teenagers.